Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics最新文献_第2页

In Silico Structure Based Designing of Dihydrofolate Reductase Enzyme Antagonists and Potential Small Molecules That Target DHFR Protein to Inhibit the Folic Acid Biosynthetic Pathways 基于硅结构设计的二氢叶酸还原酶拮抗剂和靶向DHFR蛋白抑制叶酸生物合成途径的潜在小分子

Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics Pub Date : 2017-12-07 DOI: 10.1145/3156346.3156358

Mohammad Kawsar Sharif Siam, M. Hossain, E. Kabir, Samiul Alam Rajib

{"title":"In Silico Structure Based Designing of Dihydrofolate Reductase Enzyme Antagonists and Potential Small Molecules That Target DHFR Protein to Inhibit the Folic Acid Biosynthetic Pathways","authors":"Mohammad Kawsar Sharif Siam, M. Hossain, E. Kabir, Samiul Alam Rajib","doi":"10.1145/3156346.3156358","DOIUrl":"https://doi.org/10.1145/3156346.3156358","url":null,"abstract":"Cancer has several pathways by which it is developed in our body. Among them folic acid biosynthetic pathway is one where dihydrofolate reductase (DHFR) enzyme converts dihydrofolate into tetrahydrofolate which leads to unwanted and uncontrollable growth of tissues. Our aim of this study is to design DHFR antagonistic potential small molecules that inhibits Folic Acid Biosynthetic Pathways. In this study, Human DHFR obtained from Protein Data Bank (PDB) docked with several established anticancer drugs including Afatinib, Doxorubicin, Trimetrexate, Curcumin & Trimethoprim and several potential small molecules including Acarbose, Adenosine monophosphate, Abacavir, Aceprometazine & Isoxyl; obtained from PubChem and Drug Bank respectively. PyMOL and PyRx were used to visualize, curate and dock. For validation purpose Discovery Studio and Ramachandran Plot were run. Results after docking showed best binding affinities of established anticancer drugs with Human DHFR throughout the generations for example Methotrexate to Trimethoprim. Potential small molecules which belong from different therapeutic classes.","PeriodicalId":415207,"journal":{"name":"Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124860126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Modelling and Formal Verification of Neuronal Archetypes Coupling 神经元原型耦合的建模与形式化验证

Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics Pub Date : 2017-12-07 DOI: 10.1145/3156346.3156348

Elisabetta De Maria, Thibaud L'Yvonnet, D. Gaffé, Annie Ressouche, F. Grammont

{"title":"Modelling and Formal Verification of Neuronal Archetypes Coupling","authors":"Elisabetta De Maria, Thibaud L'Yvonnet, D. Gaffé, Annie Ressouche, F. Grammont","doi":"10.1145/3156346.3156348","DOIUrl":"https://doi.org/10.1145/3156346.3156348","url":null,"abstract":"In the literature, neuronal networks are often represented as graphs where each node symbolizes a neuron and each arc stands for a synaptic connection. Some specific neuronal graphs have biologically relevant structures and behaviors and we call them archetypes. Six of them have already been characterized and validated using formal methods. In this work, we tackle the next logical step and proceed to the study of the properties of their couplings. For this purpose, we rely on Leaky Integrate and Fire neuron modeling and we use the synchronous programming language Lustre to implement the neuronal archetypes and to formalize their expected properties. Then, we exploit an associated model checker called kind2 to automatically validate these behaviors. We show that, when the archetypes are coupled, either these behaviors are slightly modulated or they give way to a brand new behavior. We can also observe that different archetype couplings can give rise to strictly identical behaviors. Our results show that time coding modeling is more suited than rate coding modeling for this kind of studies.","PeriodicalId":415207,"journal":{"name":"Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics","volume":"83 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126221675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Position-Residue Specific Dynamic Gap Penalty Scoring Strategy for Multiple Sequence Alignment 基于位置残基的多序列比对动态间隙惩罚计分策略

Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics Pub Date : 2017-12-07 DOI: 10.1145/3156346.3156354

Sanjay S. Bankapur, Nagamma Patil

{"title":"Position-Residue Specific Dynamic Gap Penalty Scoring Strategy for Multiple Sequence Alignment","authors":"Sanjay S. Bankapur, Nagamma Patil","doi":"10.1145/3156346.3156354","DOIUrl":"https://doi.org/10.1145/3156346.3156354","url":null,"abstract":"Multiple Sequence Alignment (MSA) is a basic tool for biological sequence analysis and also a crucial step utilized by biologists to analyze phylogentic, gene regulations, homology marker, drug discovery, and predicting the protein structure and its functions. Effective Alignment of multiple sequences having biologic relevance is still an open problem. Accuracy of MSA is highly dependent on the scoring function, which aligns a given residue to its appropriate position during alignment. Scoring function has three possible cases to score a pair of residues: i) a residue with same residue, ii) a residue with different residue and iii) a residue with gap. A number of biological meaningful approaches are developed for the first two cases. However, for the third case, most of the approaches follow the default score for gap penalty, which is provided as an input by an expert. In this study, we propose a new, biologically relevant, and position-residue specific dynamic scoring approach for gap penalty. Position-Residue Specific Dynamic Gap Penalty (PRSDGP) scoring function is tested on the BAliBASE benchmark dataset. The proposed PRSDGP scoring approach is compared with the CLUSTAL O program and Quality metric improvement ranges from 46.2% to 81.5%.","PeriodicalId":415207,"journal":{"name":"Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123615211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Estimating respiration rate using an accelerometer sensor 使用加速度计传感器估计呼吸速率

Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics Pub Date : 2017-12-07 DOI: 10.1145/3156346.3156349

P. D. Hung

引用次数: 13

Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics 第八届计算系统生物学与生物信息学国际会议论文集

Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics Pub Date : 1900-01-01 DOI: 10.1145/3156346

引用次数: 0